Abstract: A distinct class of infectious agents, the virophages1 that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome2 of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements3, the transpovirons4. The transpovirons are linear DNA elements of ∼7 kb [kilobases]5 that encompass six to eight protein-coding genes, two of which are homologous6 to virophage genes. Fluorescence7in situ hybridization8 showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate9 in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns10 and inteins11 constitute the complex, interconnected mobilome12 of the giant viruses and are likely to substantially contribute to interviral gene transfer.

Mobile genetic elements (MGEs) that are collectively referred to as the “mobilome” are key players in the genome evolution of prokaryotes (*1*) and eukaryotes (*2*, *3*) and are considered “genetic engineers” of biological innovation (*1*). MGEs can be roughly grouped into four major classes: transposable elements (TEs), plasmids, viruses, and self-splicing elements such as group I and II introns and inteins (*4*). The mobilomes of many bacteria, archaea, and unicellular eukaryotes include all of these elements in a free or integrated form. Given that viruses constitute a part of the mobilome, they are not normally considered to possess mobilomes of their own. However, some large viruses contain retrovirus sequences integrated into their genomes (*5*, *6*), whereas others, including members of the Mimiviridae family, harbor self-splicing introns and/or inteins (*7*, *8*, *9*). Furthermore, many viruses support the reproduction of satellite viruses1 (*10*). The discovery of the Sputnik virophage in 2008 added a new twist to the existing understanding of the relationships between different mobile elements by demonstrating for the ﬁrst time that a giant virus could be infected by another, much smaller virus in a manner similar to the viral infection of cells (11). The Sputnik virophage is a small icosahedral virus (74 nm in diameter) that parasitizes on Mamavirus, a member of the Mimiviridae family (12, 13). Sputnik replicates inside Mamavirus or Mimivirus viral factories when the host giant virus is grown in amoebae such as Acanthamoeba castellanii or A. polyphaga (11). An in-depth analysis of the Sputnik proteins has suggested an evolutionary connection between this virophage and a distinct class of TEs (14). The second virophage, the Mavirus (15), was isolated as a parasite of a distinct member of the Mimiviridae family, Cafeteria roenbergensis virus (CroV) [Previously on Metafilter] (16). At least four Mavirus proteins, including the major capsid protein13, are homologous6 to proteins of Sputnik. In addition, the Mavirus genome encodes a retroviral-type integrase and a protein-primed DNA polymerase B; these proteins are homologous to the respective proteins of Maverick/polinton DNA transposons, which insert into genomes of diverse eukaryotes, suggesting an evolutionary link between the Mavirus and the polintons (15). The third complete virophage genome sequence has been identiﬁed in the metagenome of the hypersaline Organic Lake in Antarctica (*17*). This Organic Lake virophage (OLV) is thought to parasitize on phycoDNAviruses that infect green algae. The OLV genome encodes seven proteins with homologs in Sputnik (*17*), including two key proteins, the major capsid protein and the DNA-packaging ATPase, that are shared by all three virophages. Thus, the virophages apparently share a common origin, although each underwent multiple gene replacements. The virophages are likely to be common parasites of nucleocytoplasmic large DNA viruses that infect diverse eukaryotes, and show multiple evolutionary connections to other mobile elements (*18*). Here we present ﬁndings that substantially expand the complexity of the giant virus mobilome through the description of an integrated form of the virophage and of a distinct class of MGEs, the transposovirons.

Discussion:

The discovery of the Mimivirus and subsequent identiﬁcation of other giant viruses revealed unexpected complexity of viral genomes that, with over 1,000 protein-coding genes, are more complex than many parasitic and symbiotic bacteria and are comparable to the most compact genomes of free-living bacteria and archaea (*7*). The present work shows that giant viruses are associated with a commensurately complex mobilome that encompasses three of the four major classes of mobile elements, namely self-splicing elements, transposable elements or linear plasmids (transpovirons), and viruses (virophages that can form provirophages after integration into the host giant virus genome). Different components of the giant virus mobilome share homologous genes, and genomic comparisons point to DNA transfer between the mobilome components and the host virus but also within the mobilome itself. Thus, the giant virus mobilome is a network that potentially could provide routes and vehicles for gene exchange and might make substantial contributions to the shaping of mosaic viral genomes. The giant viruses and their mobilomes together are part of even more expansive, dynamic genetic networks: the amoebae with their diverse bacterial parasites and symbionts and their own viruses (30).

Of special note is the transpoviron, a distinct plasmid that depends on giant viruses for its replication and spread. Substantial analogies can be found between the transpovirons and virus-associated plasmids present in bacteria and archaea. In particular, the well-studied bacteriophage P4 (also known as a “phasmid”) is a plasmid that replicates episomally in the absence of the helper bacteriophage P2 but is encapsidated into virions and thus can infect new bacterial cells in the presence of the helper (*31*, *32*). A similar replication strategy has been described for the archaeal virus plasmid pSSVx that depends on the fuselloviruses SSV1 or SSV2 and appears to have acquired genes from a fusellovirus (33). The discovery of the transpoviron shows that virus-associated plasmids exist in all three domains of cellular life.

It is unlikely that the present study exhausts the diversity of the giant virus mobilome; additional virophages and transpovirons, and perhaps distinct classes of mobile elements, are likely to be discovered. Indeed, the transpoviron had not been detected until the isolation of Lentille virus from a human sample described here. Furthermore, we failed to detect closely related homologs of transpoviron genes in the available databases of environmental sequences, although close homologs of many Mimivirus and Sputnik genes were readily detectable (11). Thus, speciﬁc conditions and/or habitats could be required for accumulation of transpovirons and probably other elements comprising the giant virus mobilome. Characterization of such conditions will likely lead to the discovery of additional genetic elements associated with giant viruses and facilitate elucidation of their replication mechanisms and the relationships between different mobilome components.

2Integrated Genome: A prophage is a phage (viral) genome inserted and integrated into the circular bacterial DNA chromosome. A prophage, also known as a temperate phage, is any virus in the lysogenic cycle; it is integrated into the host chromosome or exists as an extrachromosomal plasmid. Technically, a virus may be called a prophage only while the viral DNA remains incorporated in the host DNA. This is a latent form of a bacteriophage, in which the viral genes are incorporated into the bacterial chromosome without causing disruption of the bacterial cell. Upon detection of host cell damage, such as UV light or certain chemicals, the prophage is excised from the bacterial chromosome in a process called prophage induction. After induction, viral replication begins via the lytic cycle. In the lytic cycle, the virus commandeers the cell's reproductive machinery. The cell may fill with new viruses until it lyses or bursts, or it may release the new viruses one at a time in a reverse endocytotic process. The period from infection to lysis is termed the latent period. A virus following a lytic cycle is called a virulent virus. Prophages are important agents of horizontal gene transfer, and are considered part of the mobilome.

6Homology: Homologous traits of organisms are due to sharing a common ancestor, and such traits often have similar embryological origins and development. This is contrasted with analogous traits: similarities between organisms that were not present in the last common ancestor of the taxa being considered but rather evolved separately. An example of analogous traits would be the wings of bats and birds, which evolved separately but both of which evolved from the vertebrate forelimb and therefore have similar early embryology. Whether or not a trait is homologous depends on both the taxonomic and anatomical levels at which the trait is examined. For example, the bird and bat wings are homologous as forearms in tetrapods. However, they are not homologous as wings, because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods. By definition, any homologous trait defines a clade—a monophyletic taxon in which all the members have the trait (or have lost it secondarily); and all non-members lack it

7Fluorescence: The emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation. However, when the absorbed electromagnetic radiation is intense, it is possible for one electron to absorb two photons; this two-photon absorption can lead to emission of radiation having a shorter wavelength than the absorbed radiation. The emitted radiation may also be of the same wavelength as the absorbed radiation, termed "resonance fluorescence".

10Intron: An intron is any nucleotide sequence within a gene that is removed by RNA splicing while the final mature RNA product of a gene is being generated. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation. The word intron is derived from the term intragenic region; i.e., a region inside a gene. Although introns are sometimes called intervening sequences, the term "intervening sequence" can refer to any of several families of internal nucleic acid sequences that are not present in the final gene product, including inteins, untranslated sequences (UTR), and nucleotides removed by RNA editing, in addition to introns.

11Intein: An intein is a segment of a protein that is able to excise itself and rejoin the remaining portions (the exteins) with a peptide bond. Inteins have also been called "protein introns".

12Mobilome: The total of all mobile genetic elements in a genome; a play on the word Genome.

13Major Capsid Protein: A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic material of the virus.

Reviewer Comment: This post contains insufficient cowbell and should be summarily dismissed

Response: We agree that, historically, there has been a great need for additional cowbell in MetaFilter posts, however, this post both acknowledges the great contributions that cowbell has provided for MeFite studies and is entirely orthogonal to it.

Reviewer Comment: This post is a SLYT, all purveyors of SLYT posts should be dragged out and shot (Actual phrase I've seen used in a reviewer comment - the reviewer was upset about the wide angle magnification of a TEM micrograph having failed to understand the purpose of the micrograph)

Response: We agree with the criticism and have added fluff on lines 4 through 118posted by Blasdelb at 4:52 PM on October 16, 2012 [10 favorites]

If something is you'll probably find their stuff in a Bdelloid Rotifer

That abstract introduced me to the wonderful word spliceosome. Now I'm sorry I didn't study microbiology, but a good 30% of my school's undergrad population were boring, disaffected, pre-med bio majors.posted by Nomyte at 5:11 PM on October 16, 2012

I'm gonna favorite this. and then attempt to and probably fail at understanding it.posted by ninjew at 5:36 PM on October 16, 2012

I think this post is playing host to several other posts which are themselves infected by other posts...

How come those little virusites get their own mobile 'ome? What's wrong with a tent? Sheesh, phages and virons today have it so easy.posted by BlueHorse at 7:29 PM on October 16, 2012 [1 favorite]

Big fleas have little fleas,
Upon their backs to bite 'em,
And little fleas have lesser fleas,
and so, ad infinitum.posted by awenner at 7:58 PM on October 16, 2012 [1 favorite]

I love the absolute genetic promiscuity of viruses. You want some DNA? Not same species? No problem, take and do what you can with it. This must be where evolution boils the hottest.posted by CautionToTheWind at 1:37 AM on October 17, 2012

Would it be at all feasible to engineer (or conceivably, discover in the wild) a virophage or bacteriophage that could be used therapeutically? Is it possible there's some phage that's highly pathogenic to our pathogens, and could be used to help kill off (for example) AIDS in an infected human?posted by Sleeper at 9:53 AM on October 17, 2012

About the same time I posted that I discovered the Wikipedia article "phage therapy":

http://en.wikipedia.org/wiki/Phage_therapy

Looks like it's an idea that's only a little older than the discovery of phages themselves, but hasn't yet produced much in the way of useful results, in part because little research has been devoted to it.

I'm curious about the danger of creating a "there was an old lady who swallowed a fly" situation with phage therapy.posted by Sleeper at 10:09 AM on October 17, 2012

"Would it be at all feasible to engineer (or conceivably, discover in the wild) a virophage or bacteriophage that could be used therapeutically? Is it possible there's some phage that's highly pathogenic to our pathogens, and could be used to help kill off (for example) AIDS in an infected human?"

Oh Jesus Christ, I am a phage biologist who needs to go to bed.

Phages are just about the most awesome things ever but they can't infect AIDS, which doesn't have any known satellite viruses. They can however infect bacterial pathogens:

After he and his brother lost family's fortune on a doomed chocolate factory, he left for South America where he made a decent living inventing new processes for converting tropical plants such as bananas and sisal into distilled liquor for western markets. However, while he was in Mexico he noticed something interesting, after the the swarms of locusts that devastated local agriculture passed through, sick locusts could be noticed to have been left behind. It occurred to him to isolate the pathogen to see if he could use it to combat the swarms. His technique ended up working so well that in 1911 d'Herelle was invited to travel to Argentina as a microbiologist to address the locust problems there.

The problem was MASSIVE, every other year locusts would create the modern equivalent of billions of dollars worth of damage to cash crops and generate famine on the extraordinarily fertile pampas. It was so bad, and Argentina was rich enough then, that plans were being drawn up to import most of the world’s silver to build massively long 4 meter high walls across the pampas to stop the plagues. Apparently they'd have done it to if they thought they could stop theft, and on top of this the Ministry of Agricultural Defense had grown to a 3,000 member strong bureaucracy dedicated to extraordinary campaigns to defeat them.

d'Herelle's plan was again to spread diseases of the locust itself ahead of the swarms to use the same terrifying scale that made farmers so helpless, against the plague. He ended up getting funding to find sick locusts, cultivate the disease though serial transfer between 100 locust cages, and thus isolate 100% virulent and contagious strains of a cocobacillus. When thousands of these carcasses were spread out ahead of a swarm they were brought to an epic halt within a few days. After two years of d'Herelle's efforts the plagues ceased to be the issue that they once were in Argentina and the Pasteur Institute sent out his cultures to Columbia where several successful trials were conducted, as well as Cyprus and Algeria where they had significant effect.

All of this must have primed him to the idea that pathogens, or at least problem species, might have their own pathogens that we could team up with for productive effects, thus perhaps contributing to one of the most brilliant examples of deductive reasoning in modern science. At one point while he was in Paris before 1917, d'Herelle noticed something odd in a lawn of dysentery bacteria he had grown on a petri dish, a glassy clear dead spot. He must have thought this was interesting and so he plucked the spot from the plate and spread it out over a new lawn of the same bacteria, which then would not grow. Presumably figuring that he had isolated a new toxin of some kind, he made serial dilutions of it to see how just how toxic it was, and it did something toxins had never been known to do before. Arranging the plates in a row from highest dilution to lowest dilution, for a toxin, one would expect to see progressively but evenly damaged growth as one went down the series. However he saw first low numbers and then high numbers of the same glassy spots that mathematically followed the series. He quickly made a leap of judgment that would be challenged by many of the finest minds in the word until he was proven right by one of the first electron micrographs ever taken, that this wasn't a toxin at all, but a discrete organism. The problem was that his phages were far too small to see with a light microscope, no matter how powerful, as visible light has a wavelength of around 600nm and phage are around 25-250nm (thus using light to get a sense of what phage look like is kind of like using the blunt end of a telephone pole to get a sense of what a grasshopper feels like).

While d'Herelle continued to work with phages, which I will get back to later, the next big advances in understanding what phages really are would wait almost a decade for a mass movement of out of work physicists who, having suddenly run out of things to do when we figured out to much of physics, came to biology the 1920s to the 1930s. They brought with them a mechanistic view of how the universe works that they used to cause massive transformations in how we understand and interact with biology, and most used phages. One of the most influential of these scientific interlopers was a charismatic guy named Max Delbrück who quickly reasoned that, if we were ever going to understand how life works, we would need to start with the simplest organism possible and work our way up. He isolated seven bacteriophages against E. coli B, originally just his lab strain, and named them in a series T1 (previously) through T7. The central idea was that he and his growing number of colleagues1 would focus on truly understanding how these phages worked and use that knowledge to generalize to Escherichia coli, then the mouse, and then us. An essential component of this was the "Phage Treaty" among researchers in the field, which Delbrück organized in order to limit the number of model phage and hosts so that folks could meaningfully compare results. What came out of their original focus on these phages, in many respects encapsulated in Erwin Schrödinger's What is life?, has shed light on so much as to truly redefine our self-understanding as a species, much less medicine:

The Luria–Delbrück experiment elegantly demonstrated that in bacteria genetic mutations arise in the absence of selection, rather than being a response to selection. Evolutionary biology has made so much more sense ever since.

Most of the central dogma, was also figured out using phage, from most of the functions of RNA to the triplicate nature of codons

So many of the enzymes, molecular tools, we now take for granted come from phage

Delbrück turned out to be absolutely right to start simple, and his branch of Biophysics turned into molecular genetics (as opposed to the Drosophila variety) and split off into modern genetics, molecular biology, protein biology, molecular physiology, bioengineering, as well as genomics and the various other –omics. It all started with phage, but around the 70s phage biology did start to die as old professors dies and retired while their students became leaders in all of these new and exciting fields. However, I promised I’d get back to d’Herelle.

His discovery of phages was long before antibiotics, when bacterial disease killed almost everyone eventually and in horrific ways without much anyone could do for the sick. d'Herelle instantly saw the value that this pathogen of bacteria could have for patients, just like the value his coccobacilli had for farmers. He soon found a chicken farm with chicken typhoid that he successfully treated with phage isolated from the farm itself. He then isolated bacteria from the stool of a bunch dying French cavalrymen at a military hospital, isolated phage against them, amplified those phages, purified them as best he could, drank a bunch to demonstrate safety, and then gave it to the cavalrymen who each very quickly recovered.

Phage therapy exploded quickly, the major pharmaceutical companies of the United States and Europe, including Eli Lily which is still around, pumped out cocktails as quickly as they could and marketed them aggressively. However, no one really knew what phages were, much less how they worked, and most of the commercial entities profiting from phage didn’t seem to much care. This ended up giving phage a very well deserved bad reputation among physicians who tried preparations that we now know to have been heat or acid killed, or against the wrong pathogen, or against the right pathogen but with the wrong host range, or advertised as being effective against absurd things like gallstones and herpes and understandably decided the whole thing was bullshit. Many physicians considered the question settled with a pretty damning article series published in JAMA in 19342, before antibiotics became available a few years later making the question at least seem largely irrelevant for most pathogens (Though successful phage therapy of typhoid fever continued in the 50s when effective antibiotics were finally found against S. typhii, and in France until the 80’s when poorly worded AIDS related legislation killed it).

Phage therapy did, however, survive and thrive in the Soviet Union after Stalin ended up reading d’Herelle’s first two books in the early 1930s with great interest. In 1934 he invited d’Herelle to set up a phage institute in what is now the Republic of Georgia with a Georgian microbiologist, George Eliava, for the purpose of studying phage and providing the Red Army with a reliable supply. While d’Herelle is said to have been initially enamored with communism, he was soon soured on it when Eliava was suddenly kidnapped, murdered, and denounced by Beria (it likely had as much to do with Beria demonstrating that even Heroes of Soviet Science were not immune to his power as anything else, but the oral history remembered by Georgian phage biologists is that Eliava slept with an opera singer that Beria had his eye on). Despite the institute’s decapitation with the loss of Eliava and the fleeing of d’Herelle, the women they trained took over and turned it into one of the great centers of Soviet medicine. They conducted large and well-designed, particularly for the era, studies to establish phage as a standard of care and then slowly expanded that standard as new needs arose.

Over the last fifteen years or so, with the breakup of the Soviet Union and the exponentially growing crisis of antibiotic resistance, phage therapy is looking very exciting again. Unlike the ‘30s, we now have a decent understanding of phage biology as well as the infrastructure to keep phages cold until use, effective diagnostic tools, and most importantly, regulatory structures that shut out hucksters. The need is also dire, for example multi-drug resistant Staph infections kill more people in the United States than AIDS does.

Basic phage biology has also been undergoing a resurgence as we discover just how important phages are to the global ecosystem, they are indeed the dominant organism on Earth outnumbering anything else by two orders of magnitude. Indeed, despite being just ~125 nm tall (check this out for scale), if one were to stack the 1031 phages on the planet end to end you would get a tower that would stand 200 million lightyears tall. Our oceans are remarkably free of cellular life and the reason is phages, as well as the other the viruses of microbes. For example the growth and death of algae blooms are centrally mediated by viral dynamics. Meta-genomics studies of the oceans pull out more predicted phage proteins than anything else without some fancy filtering, and even then they get a bunch. Phages are also teaching us a lot about the primordial origins of life, they are after all proto-cellular organisms.

1Frank Stahl famously wrote: "The Phage Church, as we were sometimes called, was led by the Trinity of Delbrück, Luria, and Hershey. Delbrück's status as founder and his ex-cathedra manner made him the pope, of course, and Luria was the hard-working, socially sensitive priest-confessor. And Al (Hershey) was the saint."

A couple of dumb questions about phage(s): 1. Do you pronounce it fayj or fahj? and 2. Is phage singular or plural? (Or is it short for "phage therapy"?)

I've had these questions ever since I heard a Science Friday on phage therapy. The Russian (I think) gentleman pronounced it fahj, and used it like a plural, e.g. "this is what phage can do". I wasn't sure if the former was just his accent, and the latter from the lack of articles in Russian.posted by phliar at 4:36 PM on October 17, 2012

"1. Do you pronounce it fayj or fahj?"

It depends on the speaker, both are standard. I've noticed that folks from commonwealth countries, and particularly Australia, are more likely to say fahj while just about everyone else says fayj. The Dutch and Flemish say faag.

"2. Is phage singular or plural?"

Phage is short for bacteriophage, from the original name given to them in French by D'Herelle. Generally phage is considered to be correct as either singular or plural unless you are referring to a multiple of distinct phage particles - at which point the multiple particles are referred to as phages. If you think thats weird just look a the difference between virus, viruses, virii, virion, and virions.

This is badass. Thanks for the FPP and subsequent comments, Blasdelb.posted by Sleeper at 8:28 PM on October 17, 2012 [1 favorite]

I've finally processed this.

Nature is bad-ass. The ultimate battlefield. That creatures as complex as us have managed to hold together a semblance of self and species-ness in the face of relentless invasion and destruction from cosmic rays, heavy metals and other toxins, oxidation and other chemical attacks, plasmids, viruses, bacteria, amoebae, and then up to multi-cellular parasites, and then things that feed on us and eat us and use us as transport mechanisms.... it's Sparta, but for reals reals.

And I have figured out why we die! Why everything dies.

It is just the same reason why every two years you should format your PC hard drive. Because after a certain amount of time the cruft and breakage and wastage and disease builds up to such a point that the original functionality is damaged to the point where the best use of the resources embodied is to simply break it up into its smallest components and rebuild it from molecules once again.

Which means, dear friends, that in the end we are all scratch monkeys.posted by seanmpuckett at 4:44 AM on October 18, 2012

So to sum up: Her eyeball had an amoebic infection, which had a giant virus infection, which had a lysogenic virophage infection, which had a transpoviron infection.

I desperately want one of these articles to end with, "Unconfirmed reports indicate that the patient then attempted to remediate her condition by swallowing a fly."posted by eritain at 6:42 AM on October 19, 2012 [1 favorite]

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